Unravelling the complex interplay of cuproptosis, lncRNAs, and immune infiltration in Alzheimer’s disease: a step towards novel therapeutic targets

References

• Ahmad W, Ebert PR. 2021. Suppression of a core metabolic enzyme dihydrolipoamide dehydrogenase (Dld) protects against amyloid beta toxicity in C. elegans model of Alzheimer’s disease. Genes Dis. 8(6):1–12. doi: 10.1016/j.gendis.2020.08.004.
   PubMed Web of Science ®Google Scholar
• Ahmad W. 2018. Dihydrolipoamide dehydrogenase suppression induces human tau phosphorylation by increasing whole body glucose levels in a C. elegans model of Alzheimer’s disease. Exp Brain Res. 236(11):2857–2866. doi: 10.1007/s00221-018-5341-0.
   PubMed Web of Science ®Google Scholar
• Arisi I, D’Onofrio M, Brandi R, Felsani A, Capsoni S, Drovandi G, Felici G, Weitschek E, Bertolazzi P, Cattaneo A, et al. 2011. Gene expression biomarkers in the brain of a mouse model for Alzheimer’s disease: mining of microarray data by logic classification and feature selection. J Alzheimers Dis. 24(4):721–738. doi: 10.3233/jad-2011-101881.
   PubMed Web of Science ®Google Scholar
• Asadi MR, Hassani M, Kiani S, Sabaie H, Moslehian MS, Kazemi M, Ghafouri-Fard S, Taheri M, Rezazadeh M. 2021. The perspective of dysregulated Lncrnas in Alzheimer’s disease: a systematic scoping review. Front Aging Neurosci. 13:709568. doi: 10.3389/fnagi.2021.709568.
   PubMed Web of Science ®Google Scholar
• Atwood CS, Scarpa RC, Huang X, Moir RD, Jones WD, Fairlie DP, Tanzi RE, Bush AI. 2000. Characterization of Copper interactions with Alzheimer amyloid beta peptides: identification of an attomolar-affinity Copper binding site on amyloid beta1-42. J Neurochem. 75(3):1219–1233. doi: 10.1046/j.1471-4159.2000.0751219.x.
   PubMed Web of Science ®Google Scholar
• Bahn G, Jo DG. 2019. Therapeutic approaches to Alzheimer’s disease through modulation of Nrf2. Neuromolecular Med. 21(1):1–11. doi: 10.1007/s12017-018-08523-5.
   PubMed Web of Science ®Google Scholar
• Baik SH, Kang S, Son SM, Mook-Jung I. 2016. Microglia contributes to plaque growth by cell death due to uptake of amyloid B in the brain of Alzheimer’s disease mouse model. Glia. 64(12):2274–2290. doi: 10.1002/glia.23074.
   PubMed Web of Science ®Google Scholar
• Banerjee K, Munshi S, Xu H, Frank DE, Chen H-L, Chu CT, Yang J, Cho S, Kagan VE, Denton TT, et al. 2016. Mild mitochondrial metabolic deficits by Α-ketoglutarate dehydrogenase inhibition cause prominent changes in intracellular autophagic signaling: potential role in the pathobiology of Alzheimer’s disease. Neurochem Int. 96:32–45. doi: 10.1016/j.neuint.2016.02.011.
   PubMed Web of Science ®Google Scholar
• Barkova EN, Petrov AV. 1976. The influence of oxygen barotherapy on erythropoiesis in the recuperative period of hemorrhagic collapse]. Biull Eksp Biol Med. 81(2):156–158.
   PubMedGoogle Scholar
• Beason-Held LL, Goh JO, An Y, Kraut MA, O’Brien RJ, Ferrucci L, Resnick SM. 2013. Changes in brain function occur years before the onset of cognitive impairment. J Neurosci. 33(46):18008–18014. doi: 10.1523/JNEUROSCI.1402-13.2013.
   PubMed Web of Science ®Google Scholar
• Braschi B, Denny P, Gray K, Jones T, Seal R, Tweedie S, Yates B, Bruford E. 2019. Genenames.Org: the Hgnc and Vgnc resources in 2019. Nucleic Acids Res. 47(D1):D786–D792. doi: 10.1093/nar/gky930.
   PubMed Web of Science ®Google Scholar
• Brown AM, Gordon D, Lee H, Wavrant-De Vrièze F, Cellini E, Bagnoli S, Nacmias B, Sorbi S, Hardy J, Blass JP, et al. 2007. Testing for linkage and association across the dihydrolipoyl dehydrogenase gene region with Alzheimer’s Disease in three sample populations. Neurochem Res. 32(4-5):857–869. doi: 10.1007/s11064-006-9235-3.
   PubMed Web of Science ®Google Scholar
• Cao M, Li H, Zhao J, Cui J, Hu G. 2019. Identification of age- and gender-associated long noncoding Rnas in the human brain with Alzheimer’s disease. Neurobiol Aging. 81:116–126. doi: 10.1016/j.neurobiolaging.2019.05.023.
   PubMed Web of Science ®Google Scholar
• Choe YM, Suh G-H, Lee BC, Choi I-G, Lee JH, Kim HS, Kim JW. 2022. Association between Copper and global cognition and the moderating effect of iron. Front Aging Neurosci. 14:811117. doi: 10.3389/fnagi.2022.811117.
   PubMed Web of Science ®Google Scholar
• Dai B, Sun F, Cai X, Li C, Liu H, Shang Y. 2021. Significance of Rna N6-methyladenosine regulators in the diagnosis and subtype classification of childhood asthma using the gene expression omnibus database. Front Genet. 12:634162. doi: 10.3389/fgene.2021.634162.
   PubMed Web of Science ®Google Scholar
• Dai XL, Sun YX, Jiang ZF. 2006. Cu(II) potentiation of Alzheimer Abeta1-40 cytotoxicity and transition on its secondary structure. Acta Biochim Biophys Sin (Shanghai)). 38(11):765–772. doi: 10.1111/j.1745-7270.2006.00228.x.
   PubMed Web of Science ®Google Scholar
• Davies DA, Adlimoghaddam A, Albensi BC. 2021. Role of Nrf2 in synaptic plasticity and memory in Alzheimer’s disease. Cells. 10(8):1884. doi: 10.3390/cells10081884.
   PubMed Web of Science ®Google Scholar
• Denny P, Feuermann M, Hill DP, Lovering RC, Plun-Favreau H, Roncaglia P. 2018. Exploring autophagy with gene ontology. Autophagy. 14(3):419–436. doi: 10.1080/15548627.2017.1415189.
   PubMed Web of Science ®Google Scholar
• Ejaz HW, Wang W, Lang M. 2020. Copper toxicity links to pathogenesis of Alzheimer’s disease and therapeutics approaches. Int J Mol Sci. 21(20):7660.
   Web of Science ®Google Scholar
• Gibson GE, Chen HL, Xu H, Qiu L, Xu Z, Denton TT, et al. 2012. Deficits in the mitochondrial enzyme Α-ketoglutarate dehydrogenase lead to Alzheimer’s disease-like calcium dysregulation. Neurobiol Aging. 33(6):1121 e13–24.
   Web of Science ®Google Scholar
• Giulian D. 1999. Microglia and the immune pathology of Alzheimer disease. Am J Hum Genet. 65(1):13–18. doi: 10.1086/302477.
   PubMed Web of Science ®Google Scholar
• Huang HY, Lin YC, Li J, Huang KY, Shrestha S, Hong HC, et al. 2020. Mirtarbase 2020: updates to the experimentally validated microrna-target interaction database. Nucleic Acids Res. 48(D1):D148–D54.
   PubMed Web of Science ®Google Scholar
• Hudson WH, Prokhnevska N, Gensheimer J, Akondy R, McGuire DJ, Ahmed R, Kissick HT. 2019. Expression of novel long noncoding Rnas defines virus-specific effector and memory Cd8(+) T cells. Nat Commun. 10(1):196. doi: 10.1038/s41467-018-07956-7.
   PubMedGoogle Scholar
• Iasonos A, Schrag D, Raj GV, Panageas KS. 2008. How to build and interpret a nomogram for cancer prognosis. J Clin Oncol. 26(8):1364–1370. doi: 10.1200/jco.2007.12.9791.
   PubMed Web of Science ®Google Scholar
• Idda ML, Munk R, Abdelmohsen K, Gorospe M. 2018. Noncoding RNAs in Alzheimer’s disease. Wiley Interdiscip Rev Rna. 9(2):1463. doi: 10.1002/wrna.1463.
   Web of Science ®Google Scholar
• Karagkouni D, Paraskevopoulou MD, Tastsoglou S, Skoufos G, Karavangeli A, Pierros V, et al. 2020. Diana-Lncbase V3: indexing experimentally supported Mirna targets on non-coding transcripts. Nucleic Acids Res. 48(D1):D101–D10.
   PubMed Web of Science ®Google Scholar
• Kitazawa M, Yamasaki TR, LaFerla FM. 2004. Microglia as a potential bridge between the amyloid beta-peptide and tau. Ann N Y Acad Sci. 1035(1):85–103. doi: 10.1196/annals.1332.006.
   PubMedGoogle Scholar
• Knopman DS, Amieva H, Petersen RC, Chételat G, Holtzman DM, Hyman BT, Nixon RA, Jones DT. 2021. Alzheimer disease. Nat Rev Dis Primers. 7(1):33. doi: 10.1038/s41572-021-00269-y.
   PubMed Web of Science ®Google Scholar
• Li L, Xu Y, Zhao M, Gao Z. 2020. Neuro-protective roles of long non-coding Rna Malat1 in Alzheimer’s disease with the involvement of the microrna-30b/Cnr1 network and the following Pi3k/Akt activation. Exp Mol Pathol. 117:104545. doi: 10.1016/j.yexmp.2020.104545.
   PubMed Web of Science ®Google Scholar
• Liang WS, Dunckley T, Beach TG, Grover A, Mastroeni D, Walker DG, Caselli RJ, Kukull WA, McKeel D, Morris JC, et al. 2007. Gene expression profiles in anatomically and functionally distinct regions of the normal aged human brain. Physiol Genomics. 28(3):311–322. doi: 10.1152/physiolgenomics.00208.2006.
   PubMed Web of Science ®Google Scholar
• Liu J, Berthier CC, Kahlenberg JM. 2017. Enhanced inflammasome activity in systemic lupus erythematosus is mediated via type I interferon-induced up-regulation of interferon regulatory factor 1. Arthritis Rheumatol. 69(9):1840–1849. doi: 10.1002/art.40166.
   PubMed Web of Science ®Google Scholar
• Mammana S, Fagone P, Cavalli E, Basile MS, Petralia MC, Nicoletti F, Bramanti P, Mazzon E. 2018. The role of macrophages in neuroinflammatory and neurodegenerative pathways of Alzheimer’s disease, amyotrophic lateral sclerosis, and multiple sclerosis: pathogenetic cellular effectors and potential therapeutic targets. Int J Mol Sci. 19(3):831. doi: 10.3390/ijms19030831.
   PubMed Web of Science ®Google Scholar
• Marchese FP, Raimondi I, Huarte M. 2017. The multidimensional mechanisms of long noncoding Rna function. Genome Biol. 18(1):206. doi: 10.1186/s13059-017-1348-2.
   PubMed Web of Science ®Google Scholar
• Miller JA, Woltjer RL, Goodenbour JM, Horvath S, Geschwind DH. 2013. Genes and pathways underlying regional and cell type changes in Alzheimer’s disease. Genome Med. 5(5):48. doi: 10.1186/gm452.
   PubMed Web of Science ®Google Scholar
• Miller LM, Wang Q, Telivala TP, Smith RJ, Lanzirotti A, Miklossy J. 2006. Synchrotron-based infrared and X-ray imaging shows focalized accumulation of Cu and Zn co-localized with beta-amyloid deposits in Alzheimer’s disease. J Struct Biol. 155(1):30–37. doi: 10.1016/j.jsb.2005.09.004.
   PubMed Web of Science ®Google Scholar
• Moreira PI, Carvalho C, Zhu X, Smith MA, Perry G. 2010. Mitochondrial dysfunction is a trigger of Alzheimer’s disease pathophysiology. Biochim Biophys Acta. 1802(1):2–10. doi: 10.1016/j.bbadis.2009.10.006.
   PubMed Web of Science ®Google Scholar
• Naradikian MS, Hao Y, Cancro MP. 2016. Age-associated B cells: key mediators of both protective and autoreactive humoral responses. Immunol Rev. 269(1):118–129. doi: 10.1111/imr.12380.
   PubMed Web of Science ®Google Scholar
• Newman AM, Liu CL, Green MR, Gentles AJ, Feng W, Xu Y, Hoang CD, Diehn M, Alizadeh AA. 2015. Robust enumeration of cell subsets from tissue expression profiles. Nat Methods. 12(5):453–457. doi: 10.1038/nmeth.3337.
   PubMed Web of Science ®Google Scholar
• Qiu C, Kivipelto M, von Strauss E. 2009. Epidemiology of Alzheimer’s disease: occurrence, determinants, and strategies toward intervention. Dialogues Clin Neurosci. 11(2):111–128. doi: 10.31887/DCNS.2009.11.2/cqiu.
   PubMedGoogle Scholar
• Ratner B. 2009. The correlation coefficient: its values range between +1/−1, or do they? J Target Meas Anal Mark. 17(2):139–142. doi: 10.1057/jt.2009.5.
   Google Scholar
• Reiss AB, Ahmed S, Dayaramani C, Glass AD, Gomolin IH, Pinkhasov A, Stecker MM, Wisniewski T, De Leon J. 2022. The role of mitochondrial dysfunction in Alzheimer’s disease: a potential pathway to treatment. Exp Gerontol. 164:111828. doi: 10.1016/j.exger.2022.111828.
   PubMed Web of Science ®Google Scholar
• Riley RL, Khomtchouk K, Blomberg BB. 2017. Age-associated B cells (Abc) inhibit B lymphopoiesis and alter antibody repertoires in old age. Cell Immunol. 321:61–67. doi: 10.1016/j.cellimm.2017.04.008.
   PubMed Web of Science ®Google Scholar
• Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, Smyth GK. 2015. Limma powers differential expression analyses for Rna-sequencing and microarray studies. Nucleic Acids Res. 43(7):e47–e47. doi: 10.1093/nar/gkv007.
   PubMed Web of Science ®Google Scholar
• Sabaie H, Moghaddam MM, Moghaddam MM, Ahangar NK, Asadi MR, Hussen BM, Taheri M, Rezazadeh M. 2021. Bioinformatics analysis of long non-coding Rna-associated competing endogenous Rna network in schizophrenia. Sci Rep. 11(1):24413. doi: 10.1038/s41598-021-03993-3.
   PubMed Web of Science ®Google Scholar
• Sarell CJ, Wilkinson SR, Viles JH. 2010. Substoichiometric levels of Cu2+ ions accelerate the kinetics of fiber formation and promote cell toxicity of amyloid-{beta} from Alzheimer disease. J Biol Chem. 285(53):41533–41540. doi: 10.1074/jbc.M110.171355.
   PubMed Web of Science ®Google Scholar
• Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. 2003. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13(11):2498–2504. doi: 10.1101/gr.1239303.
   PubMed Web of Science ®Google Scholar
• Song MO, Mattie MD, Lee CH, Freedman JH. 2014. The role of Nrf1 and Nrf2 in the regulation of Copper-responsive transcription. Exp Cell Res. 322(1):39–50. doi: 10.1016/j.yexcr.2014.01.013.
   PubMed Web of Science ®Google Scholar
• Tang D, Chen X, Kroemer G. 2022. Cuproptosis: a Copper-triggered modality of mitochondrial cell death. Cell Res. 32(5):417–418. doi: 10.1038/s41422-022-00653-7.
   PubMed Web of Science ®Google Scholar
• Torok J, Maia PD, Powell F, Pandya S, Raj A. 2018. A method for inferring regional origins of neurodegeneration. Brain. 141(3):863–876. doi: 10.1093/brain/awx371.
   PubMedGoogle Scholar
• Tsvetkov P, Coy S, Petrova B, Dreishpoon M, Verma A, Abdusamad M, Rossen J, Joesch-Cohen L, Humeidi R, Spangler RD, et al. 2022. Copper induces cell death by targeting lipoylated Tca cycle proteins. Science. 375(6586):1254–1261. doi: 10.1126/science.abf0529.
   PubMed Web of Science ®Google Scholar
• Wang M, Qin L, Tang B. 2019. Micrornas in Alzheimer’s disease. Front Genet. 10:153. doi: 10.3389/fgene.2019.00153.
   PubMed Web of Science ®Google Scholar
• Yi J, Chen B, Yao X, Lei Y, Ou F, Huang F. 2019. Upregulation of the Lncrna Meg3 improves cognitive impairment, alleviates neuronal damage, and inhibits activation of astrocytes in hippocampus tissues in Alzheimer’s disease through inactivating the Pi3k/Akt signaling pathway. J Cell Biochem. 120(10):18053–18065. doi: 10.1002/jcb.29108.
   PubMed Web of Science ®Google Scholar
• Yin Z, Raj D, Saiepour N, Van Dam D, Brouwer N, Holtman IR, Eggen BJL, Möller T, Tamm JA, Abdourahman A, et al. 2017. Immune hyperreactivity of Aβ plaque-associated microglia in Alzheimer’s disease. Neurobiol Aging. 55:115–122. doi: 10.1016/j.neurobiolaging.2017.03.021.
   PubMed Web of Science ®Google Scholar
• Yu G, Wang LG, Han Y, He QY. 2012. Clusterprofiler: an R package for comparing biological themes among gene clusters. OMICS. 16(5):284–287. doi: 10.1089/omi.2011.0118.
   PubMed Web of Science ®Google Scholar